Beta diversity

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by timepoint (PCA):

Clustering by treatment (PCA): after removing samples from timepoint 0 # BECAUSE WE KNOW THAT AT TIMEPOINT 0 WE SHOULD NOT HAVE DIFFERENCES BETWEEN GROUPS

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Clustering by treatment (PCA): by timepoints

Time-point 28

## Warning in data.frame(..., check.names = FALSE): row names were found from a
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Time-point 21

## Warning in data.frame(..., check.names = FALSE): row names were found from a
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Time-point 8

## Warning in data.frame(..., check.names = FALSE): row names were found from a
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Time-point 0

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

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MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

Clustering by timepoint (MDS):

NMDS1 vs NMDS2

Clustering by type (MDS): NMDS1 vs NMDS3

Clustering by type (MDS): NMDS2 vs NMDS3

Clustering by treatment by timepoint (MDS):

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 1 0.3754833 0.3754833 1.702507 0.0256107 0.044
timepoint 3 1.2733871 0.4244624 1.924586 0.0868544 0.003
residuals 59 13.0122919 0.2205473 NA 0.8875348 NA
total 63 14.6611623 NA NA 1.0000000 NA

going 3D

## Run 0 stress 0.0751196 
## Run 1 stress 0.09009265 
## Run 2 stress 0.0750855 
## ... New best solution
## ... Procrustes: rmse 0.006212184  max resid 0.03108058 
## Run 3 stress 0.09253849 
## Run 4 stress 0.08672834 
## Run 5 stress 0.07508398 
## ... New best solution
## ... Procrustes: rmse 0.000255134  max resid 0.001107973 
## ... Similar to previous best
## Run 6 stress 0.0766515 
## Run 7 stress 0.07510223 
## ... Procrustes: rmse 0.003150098  max resid 0.02039621 
## Run 8 stress 0.07508376 
## ... New best solution
## ... Procrustes: rmse 0.000118586  max resid 0.0005505274 
## ... Similar to previous best
## Run 9 stress 0.07511047 
## ... Procrustes: rmse 0.005248189  max resid 0.03104522 
## Run 10 stress 0.09092367 
## Run 11 stress 0.0804885 
## Run 12 stress 0.07508375 
## ... New best solution
## ... Procrustes: rmse 0.0001163687  max resid 0.0006493131 
## ... Similar to previous best
## Run 13 stress 0.0923802 
## Run 14 stress 0.07552532 
## ... Procrustes: rmse 0.01300386  max resid 0.08560523 
## Run 15 stress 0.07511018 
## ... Procrustes: rmse 0.005201986  max resid 0.03094017 
## Run 16 stress 0.07508373 
## ... New best solution
## ... Procrustes: rmse 4.10306e-05  max resid 0.0002072934 
## ... Similar to previous best
## Run 17 stress 0.09273423 
## Run 18 stress 0.07510991 
## ... Procrustes: rmse 0.005200093  max resid 0.03090325 
## Run 19 stress 0.07510252 
## ... Procrustes: rmse 0.003164914  max resid 0.02054252 
## Run 20 stress 0.07510959 
## ... Procrustes: rmse 0.005189834  max resid 0.03085674 
## *** Solution reached

timepoint 0

timepoint 8

timepoint 21

timepoint 28